--- a/pyGenomeTracks.xml	Tue Jul 21 03:32:48 2020 -0400
+++ b/pyGenomeTracks.xml	Wed Nov 18 21:33:46 2020 +0000
@@ -21,11 +21,17 @@
         sed '/^$/d' '$tracks_config' &&
         @BINARY@
             --tracks '$tracks_config'
-            #if $region and $region is not None:
-                --region '$region'
+            --region '$region'
+            #if $global_args.title != '':
+                --title '$global_args.title'
             #end if
-            #if $global_args.title is not None:
-                --title '$global_args.title'
+            #if $global_args.plotWidth != '':
+                --plotWidth $global_args.plotWidth
+            #else:
+                --width $global_args.width
+            #end if
+            #if $global_args.height != '':
+                --height '$global_args.height'
             #end if
             --fontSize $global_args.fontsize
             --dpi $global_args.dpi
@@ -557,11 +563,17 @@
     #end if
 alpha = $track.track_file_style_conditional.alpha
 line_width = $track.track_file_style_conditional.line_width
-    #if $track.track_file_style_conditional.x_center != "":
-x_center = $track.track_file_style_conditional.x_center
+    #if $track.track_file_style_conditional.scalebar_pos.x_center != "":
+x_center = $track.track_file_style_conditional.scalebar_pos.x_center
+    #end if
+    #if $track.track_file_style_conditional.scalebar_pos.size != "":
+size = $track.track_file_style_conditional.scalebar_pos.size
     #end if
-    #if $track.track_file_style_conditional.size != "":
-size = $track.track_file_style_conditional.size
+    #if $track.track_file_style_conditional.scalebar_pos.scalebar_start_position != "":
+scalebar_start_position = $track.track_file_style_conditional.scalebar_pos.scalebar_start_position
+    #end if
+    #if $track.track_file_style_conditional.scalebar_pos.scalebar_end_position != "":
+scalebar_end_position = $track.track_file_style_conditional.scalebar_pos.scalebar_end_position
     #end if
 where = $track.track_file_style_conditional.sb_where
     #if $track.track_file_style_conditional.fontsize != "":
@@ -580,12 +592,19 @@
     <inputs>
         <!--Arguments for pgt-->
         <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false"
-            help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
+            help="The format is chr:start-end, for example chr10:10-500">
+            <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
+        </param>
         <section name="global_args" title="Configure figure parameters" expanded="False">
             <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> 
             <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>
             <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"
                    help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>
+            <param argument="--width" type="float" label="Figure width in cm" value="40"/>
+            <param argument="--plotWidth" type="float" label="Width in centimeters of the plotting (central) part" optional="true"
+                    help="This will overwrite what has been defined as a figure width."/>
+            <param argument="--height" type="float" label="Figure height in centimeters" optional="true"
+                    help="If not given, the figure height is computed based on the heights of the tracks. If given, the track height are proportionally scaled to match the desired figure height."/>
             <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"
                    min="0" max="1"/> 
             <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
@@ -964,10 +983,14 @@
                     <param name="color" type="color" label="Color of the scale bar" optional="True" />
                     <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
                     <param name="line_width" type="float" value="0.5" label="width of lines"/>
-                    <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
-                           help="If not set it will be in the middle of the plotted area."/>
-                    <param name="size" type="integer" label="size of the scale bar" optional="True"
-                           help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
+                    <section name="scalebar_pos" title="Set the scalebar position" expanded="true" help="You can optionally define one or multiple parameters below.">
+                        <param name="scalebar_start_position" type="integer" label="coordinate where the scale bar should begin." optional="True"/>
+                        <param name="scalebar_end_position" type="integer" label="coordinate where the scale bar should end." optional="True"/>
+                        <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
+                            help="If not set and cannot be deduced from others it will be in the middle of the plotted area."/>
+                        <param name="size" type="integer" label="size of the scale bar" optional="True"
+                            help="If not set and cannot be deduced from others it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
+                    </section>
                     <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar">
                         <option value="left" selected="True">left</option>
                         <option value="right">right</option>
@@ -1174,7 +1197,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 2-->
         <test>
@@ -1238,7 +1261,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 3-->
         <test>
@@ -1469,7 +1492,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 4-->
         <test>
@@ -1507,7 +1530,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 5-->
         <test>
@@ -1545,7 +1568,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 6-->
         <test>
@@ -1619,7 +1642,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 7-->
         <test>
@@ -1724,7 +1747,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 8-->
         <test>
@@ -1766,7 +1789,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 9-->
         <test>
@@ -1825,7 +1848,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 10-->
         <test>
@@ -1875,7 +1898,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 11-->
         <test>
@@ -1932,7 +1955,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 12-->
         <test>
@@ -1982,7 +2005,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 13-->
         <test>
@@ -2035,7 +2058,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 14-->
         <test>
@@ -2065,15 +2088,17 @@
                     <param name="color" value="red"/>
                     <param name="alpha" value="0.5"/>
                     <param name="line_width" value="2"/>
-                    <param name="x_center" value="3200000"/>
-                    <param name="size" value="100002"/>
+                    <section name="scalebar_pos">
+                        <param name="x_center" value="3200000"/>
+                        <param name="size" value="100002"/>
+                    </section>
                     <param name="sb_where" value="right"/>
                     <param name="fontsize" value="8"/>
                     <param name="spacer_height" value="4"/>
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 15-->
         <test>
@@ -2132,7 +2157,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 16-->
         <test>
@@ -2173,7 +2198,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="1000" />
         </test>
         <!--test 17-->
         <test>
@@ -2296,7 +2321,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 18-->
         <test>
@@ -2374,7 +2399,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 19-->
         <test>
@@ -2505,7 +2530,7 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="100" />
         </test>
         <!--test 20-->
         <test>
@@ -2555,6 +2580,7 @@
                     <param name="line_width" value="3" />
                     <param name="invert_orientation" value="true" />
                     <param name="title" value="links line_width = 3 color RdYlGn" />
+                    <param name="height" value="3" />
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -2597,6 +2623,7 @@
                     <param name="invert_orientation" value="true" />
                     <param name="use_middle" value="true" />
                     <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />
+                    <param name="height" value="3" />
                 </conditional>
             </repeat>
             <repeat name="tracks">
@@ -2607,7 +2634,86 @@
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
-            <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" />
+            <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="1200" />
+        </test>
+        <!--test 21-->
+        <test>
+            <param name="region" value="X:3000000-3600000"/>
+            <section name="global_args">
+                <param name="trackLabelFraction" value="0.3"/>
+                <param name="plotWidth" value="12"/>
+                <param name="dpi" value="20"/>
+            </section>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="scalebar where = right" />
+                    <param name="where" value="right" />
+                    <param name="spacer_height" value="0.5"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="scalebar scalebar_start_position = 3200000" />
+                    <section name="scalebar_pos">
+                        <param name="scalebar_start_position" value="3200000"/>
+                    </section>
+                    <param name="spacer_height" value="0.5"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" />
+                    <section name="scalebar_pos">
+                        <param name="scalebar_start_position" value="3200000"/>
+                        <param name="scalebar_start_position" value="3250000"/>
+                    </section>
+                    <param name="spacer_height" value="0.5"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="scalebar scalebar_start_position = 3200000 x_center = 3250000" />
+                    <section name="scalebar_pos">
+                        <param name="scalebar_start_position" value="3200000"/>
+                        <param name="x_center" value="3250000"/>
+                    </section>
+                    <param name="spacer_height" value="0.5"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="scalebar scalebar_start_position = 3200000 size = 50000" />
+                    <section name="scalebar_pos">
+                        <param name="scalebar_start_position" value="3200000"/>
+                        <param name="size" value="50000"/>
+                    </section>
+                    <param name="spacer_height" value="0.5"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="scale_bar_option" />
+                    <param name="title" value="scalebar scalebar_end_position = 3200000 size = 50000" />
+                    <section name="scalebar_pos">
+                        <param name="scalebar_end_position" value="3200000"/>
+                        <param name="size" value="50000"/>
+                    </section>
+                    <param name="spacer_height" value="0.5"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="xaxis_option" />
+                    <param name="xaxis_where" value="bottom" />
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" />
         </test>
     </tests>
     <help><![CDATA[
@@ -2619,10 +2725,12 @@
     Currently, it is possible to plot:
 
     - bigwig
-    - bed (many options)
+    - bed/gtf (many options)
     - bedgraph
-    - links (represented as arcs)
-    - Hi-C matrices
+    - epilogos
+    - narrow peaks
+    - links
+    - Hi-C matrices (cool or HiCExplorer h5)
 
 _________________
 
@@ -2631,17 +2739,21 @@
 
 This tool takes various types of tracks as input:
 
+    - **Hi-C tracks:**
+        - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
+        - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
     - **Chromatin states:** display blocks of different colors following a bed file.
-    - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.
+    - **Gene track / Bed Track:** display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off.
+    - **Link track:** display links (pair of coordinates) as arcs, triangles or loops.
+    - **NarrowPeak track:** display narrowPeak (encode format) as boxes or as curve (reconstructed peak).
     - **Bigwig track:** generic bigwig track plotting.
     - **Bedgraph track:** generic bedgraph track plotting.
     - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores).
     - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``.
+    - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks.
     - **Spacer:** Add some space between two tracks.
-    - **Hi-C tracks:**
-        - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
-        - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
-
+    - **X-axis:** Plot x-axis scale wherever you want.
+    - **Scale bar track:** Plot scale bar.
 
 For each track, parameters for the color, the width or the font size can be defined.
 
@@ -2651,7 +2763,7 @@
 ------
 
 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)
-also contains Hi-C data. The plot is composed of tracks that need to be specified.
+may also contains Hi-C data. The plot is composed of tracks that need to be specified.
 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.
 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to:
 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states,
@@ -2663,8 +2775,9 @@
 
 _________________
 
-| For more information about pyGenomeTracks please consider our documentation on github_
+| For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_
 
+.. _readthedocs: https://pygenometracks.readthedocs.io
 .. _github: https://github.com/deeptools/pyGenomeTracks
 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
 ]]></help>